The invention relates to the use of probes targeting sequences from the 5xe2x80x2 untranslated region of HCV for genotyping of HCV isolates.
The invention also relates to a process for genotyping of HCV isolates.
The invention also relates to a kit for genotyping of HCV isolates.
Hepatitis C viruses (HCV) are a family of positive-stranded, enveloped RNA viruses causing the majority of non-A, non-B (NANB) hepatitis. Their genomic organization indicates a close relationship to the Pestiviridae and Flaviviridae. The sequences of cDNA clones covering the complete genome of several prototype isolates have already been completely determined (Kato et al., 1990; Choo et al., 1991; Okamoto et al., 1991; Takamizawa et al., 1991; Okamoto et al., 1992b). These genomes are about 9500 base pairs long. The isolates reported by Kato, Takamizawa, and Choo contain an open reading frame (ORF) of 3010 or 3011 amino acids, and those reported by Okamoto encode 3033 amino acids. Comparison of these isolates shows a considerable variability in the envelope (E) and non-structural (NS) regions, while the 5xe2x80x2 untranslated region (UR) and, to a lesser extent, the core region are highly conserved.
Using cloned sequences of the NS3 region, Kubo et al. (1989) compared a Japanese and an American isolate and found nearly 80% nucleotide and 92% amino acid homology. The existence of sequence variability was further documented when sequences of the 5xe2x80x2 UR, core, and E1 regions became available HC-J1 and HC-J4; Okamoto et al., 1990). After the isolation of several NS5 fragments in Japanese laboratories, two groupes, K1 and K2, were described (Enomoto et al., 1990). A comparison of the xe2x80x9cAmerican-likexe2x80x9d isolate PT-1 with K1, which was more prevalent in Japan, showed that they represent closely related but different subtypes with an intergroup nucleotide identity of about 80%. The K2 sequence was more distantly related to both K1 and PT-1, because homologies of only 67% at the nucleic acid level, and 72% at the amino acid level were observed. Moreover, K2 could be divided into two groups, K2a and K2b, also showing intergroup nucleotide homologies of about 80%. Nucleotide sequence analysis in the 5xe2x80x2 UR showed 99% identity between K1 and PT-1, and at most 94% identity between K1 and K2, enabling the use of the 5xe2x80x2 UR for restriction fragment length polymorphism (RFLP) and classification of HCV into groups K1 and K2 (Nakao et al., 1991). Further evidence for a second group was given by the complete sequence of HC-J6 and HC-J8, two sequences related to the K2 group (Okamoto et al., 1991; Okamoto et al., 1992b). A phylogenetic tree of HCV containing four branches (i.e., Type I: HCV-1 and HCV-H; Type II: HCV-J, -BK, HC-J4; Type III: HC-J6; Type IV: HC-J8) was proposed by Okamoto et al. (1992b). However, nucleic acid sequence homologies of 79% can be observed between Type I and Type II, and also between Type III and IV. A lesser degree of relatedness between the first group (Type I and II) and the second group (Types III and IV) of only 67-68% exists. Moreover, a new type of HCV, HCV-T, was detected in Thailand after studying NS5 regions (Mori et al., 1992). HCV-T had a sequence homology of about 65% with all other known NS5 sequences, and two groups could be detected, HCV-Ta and HCV-Tb, which again exhibited nucleic acid sequence homologies of about 80%. Elucidation of the phylogenetic relationship of a similar new group found in British isolates with Type I to IV was possible by analyzing the conserved parts of the 5xe2x80x2 UR, core, NS3, and NS5 regions (Chan et al., 1992a). A new phylogenetic tree was proposed, whereby xe2x80x98type 1xe2x80x99 corresponds with Type I and II, xe2x80x98type 2xe2x80x99 with Type III and IV, and xe2x80x98type 3xe2x80x99 with their own isolates E-b1 to E-b8 and HCV-T. Some sequences of the 5xe2x80x2 UR of isolates from xe2x80x98type 3xe2x80x99 were also reported by others (Bukh et al., 1992; Cha et al., 1992; Lee et al., 1992).
Several patent applications have addressed the problem of detecting the presence of HCV by means of probes derived from the genome of type 1 HCV isolates (WO 92/02642, EP 419 182, EP 398 748, EP 469 438 and EP 461 863). Furthermore, the 5xe2x80x2 UR of HCV isolates has been proven to be a good candidate for designing probes and primers for general HCV detection (Cha et al., 1991; Inchaupse et al., 1991). However, none of these patent applications presents a method for identifying the type and/or subtype of HCV present in the sample to be analyzed.
The demonstration that different HCV genotype infections resulted in different serological reactivities (Chan et al., 1991) and responses to interferon IFN-xcex3 treatment (Pozatto et al., 1991; Kanai et al., 1992; Yoshioka et al., 1992) stresses the importance of HCV genotyping. Until now, this could only be achieved by large sequencing efforts in the coding region or in the 5xe2x80x2 UR, or by polymerase chain reactions (PCR) on HCV cDNA with type-specific sets of core primers (Okamoto et al. 1992a), or by (RFLP) analysis in the 5xe2x80x2 UR or in the NS5 region (Nakao et al., 1991; Chan et al., 1992b). However, none of these above-mentioned patent applications or publications offers a reliable method for identifying the type or subtype of HCV present in the sample to be analyzed, especially since typing is laborious and subtyping seems to be even more laborious or impossible by means of these methods. In this respect, it can be noted that Lee et al. (1992) attempt to distinguish between the HCV isolates HCV 324 and HCV 324X by means of PCR fragments from the 5xe2x80x2 UR of the genomes of these isolates. The results demonstrate that these 5xe2x80x2 UR probes do not show a specific reactivity with the genome of the respective isolate from which they were derived.
Consequently, the aim of the present invention is to provide a method for the rapid and indisputable determination of the presence of one or several genotypes of HCV present in a biological sample and indisputably classifying the determined isolate(s).
Another aim of the invention is to provide a process for identifying yet unknown HCV types or subtypes.
Another aim of the invention is to provide a process enabling the classification of infected biological fluids into different serological groups unambiguiously linked to types and subtypes at the genomic level.
Another aim of the invention is to provide a kit for rapid detection of the presence or absence of different types or subtypes of HCV.
The invention relates to the use of at least one probe, with said probe being (i) capable of hybridizing to a genotype specific target region, present in an analyte strand, in the domain extending from the nucleotides at positions xe2x88x92291 to xe2x88x9266 of the 5xe2x80x2 untranslated region (UR) of one of the HCV isolates, or with said probe being (ii) complementary to any of the above-defined probes, for genotyping HCV isolates present in a biological sample.
The invention relates to the use of at least one probe preferably containing from about 5 to about 50 nucleotides, more preferably from about 10 to about 40 nucleotides, and most preferably containing from about 15 to about 30 nucleotides, with said probe being (i) capable of liable to hybridizing to a genotype specific target region present in an analyte strand in the domain extending from the nucleotides at positions xe2x88x92291 to xe2x88x9266 of the 5xe2x80x2 UR of one of the HCV isolates represented by their cDNA sequences, for example represented by their cDNA sequences in FIG. 2, with said negative numbering of the nucleotide positions starting at the nucleotide preceding the first ATG codon of the open reading frame encoding the HCV polyprotein, or with said probe being (ii) complementary to the above-defined probes, for (in vitro) genotyping HCV isolates present in a biological sample, with said sample being possibly previously identified as being HCV positive.
The above mentioned process may be used for classifying said isolate according to the percentage of homology with other HCV isolates, according to the fact that isolates belonging to the same type:
exhibit homology of more than 74% at the nucleic acid level in the complete genome;
or exhibit homology of more than 74% at the nucleic acid level in the NS5 region between nucleotide positions 7935 and 8274;
or of which the complete polyprotein shows more than 78% homology at the amino acid level;
or of which the NS5 region between amino acids at positions 2646 and 2758 shows more than 80% homology at the amino acid level;
and according to the fact that HCV isolates belonging to the same subtype exhibit homology of more than 90% at the nucleic acid level in the complete genome and of more than 90% at the amino acid level in the complete polyprotein,
More preferably the above mentioned process relates to the classification of HCV isolates according to the fact that,
(1) based on phylogenetic analysis of nucleic acid sequences in the NS5b region between nucleotides 7935 and 8274 (Choo et al., 1991) or 8261 and 8600 (Kato et al., 1990) or 8342 and 8681 (Okamoto et al, 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.34, usually less than 0.33, and more usually of less than 0.32, and isolates belonging to the same subtype show nucleotide distances of less than 0.135, usually of less than 0.13, and more usually of less than 0.125, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.135 to 0.34, usually ranging from 0.14 to 0.33, and more usually ranging from 0.15 to 0.32, and isolates belonging to different HCV types show nucleotide distances greater than 0.34, usually greater than 0.35, and more usually of greater than 0.36,
(2) based on phylogenetic analysis of nucleic acid sequences in the core/E1 Region between nucleotides 378 and 957, isolates belonging to the same HCV type show nucleotide distances of less than 0.38, usually of less than 0.37, and more usually of less than 0.36, and isolates belonging to the same subtype show nucleotide distances of less than 0.17, usually of less than 0.16, and more usually of less than 0.15, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.15 to 0.38, usually ranging from 0.16 to 0.37, and more usually ranging from 0.17 to 0.36, and isolates belonging to different HCV types show nucleotide distances greater than 0.36, usually more than 0.365, and more usually of greater than 0.37,
(3) based on phylogenetic analysis of nucleic acid sequences in the NS3/NS4 region between nucleotides 4664 and 5292 (Choo et al., 1991) or between nucleotides 4993 and 5621 (Kato et al., 1990) or between nucleotides 5017 and 5645 (Okamoto et al., 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.35, usually of less than 0.34, and more usually of less than 0.33, and isolates belonging to the same subtype show nucleotide distances of less than 0.19, usually of less than 0.18, and more usually of less than 0.17, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.17 to 0.35, usually ranging from 0.18 to 0.34, and more usually ranging from 0.19 to 0.33, and isolates belonging to different HCV types show nucleotide distances greater than 0.33, usually greater than 0.34, and more usually of greater than 0.35.
The term xe2x80x9cgenotypingxe2x80x9d refers to either typing and/or subtyping. A method for xe2x80x98genotypingxe2x80x99 HCV isolates is considered to, at least partly, classify HCV isolates into genotypes. A HCV xe2x80x98genotypexe2x80x99 is a group of HCV isolates with related sequences. Said related sequences are defined as showing nucleotide distances as indicated above and as illustrated in example 9. Both larger groups (HCV types) and smaller groups (HCV subtypes) have been shown to be related. A HCV type always includes one or more HCV subtypes. Consequently, a method for genotyping can aim at typing (classification into HCV types) of HCV isolates without the need for subtyping (classification into HCV subtypes), or, in a preferred embodiment, subtyping can be aimed at. It should be understood that classification into subtypes inherently yields data for classification into types.
The expression xe2x80x9cgenotype specific target regionxe2x80x9d refers at least one nucleotide variation observed between different HCV genotypes in the 5xe2x80x2 untranslated region (UR) as can be readily deduced from FIGS. 2 and 4.
The term xe2x80x9cHCV polyproteinxe2x80x9d refers to the HCV polyprotein of the HCV-J isolate (Kato et al., 1990), which belongs to subtype 1b.
The expression xe2x80x9cprobexe2x80x9d corresponds to any polynucleotide which forms a hybrid with a target sequence present in a certain HCV isolate on the basis of complementarity. Such a probe may be composed of DNA, RNA, or synthetic nucleotide analogs. The probes of the invention can be incubated with an analyte strand immobilized to a solid substrate. In a preferred embodiment of the invention, the probes themselves can be immobilized to a solid substrate. These probes may further include capture probes, characterized as being coupled to a binding molecule which in turn is directly or indirectly bound to a solid substrate, or may also include label probes, characterized in that they carry a detectable label.
The invention relates to a process for genotyping HCV isolates present in a biological sample; comprising the steps of:
contacting said sample in which the ribonucleotides or deoxyribonucleotides have been made accessible, if need be, under suitable denaturation, with at least one probe, with said probe being (i) capable of hybridizing to a region in the domain extending from nucleotides at positions xe2x88x92291 to xe2x88x9266 of the 5xe2x80x2 untranslated region of one of the HCV isolates, or with said probe being (ii) complementary to any of the above-defined probes, and,
detecting the complexes possibly formed between said probe and the nucleotide sequence of the HCV isolate to be identified.
The invention relates also to a process for genotyping an HCV isolate present in a biological sample, comprising the steps of:
contacting said sample in which the ribonucleotides and deoxyribonucleotides have been made accessible, if need be, under suitable denaturation, with at least one probe from preferably from about 5 to 50, more preferably from about 10 to about 40 nucleotides most preferably from about 15 to about 30 nucleotides, with said probe being (i) capable of hybridizing to a region in the domain extending from nucleotides at positions xe2x88x92291 to xe2x88x9266 of the 5xe2x80x2 UR of one of the HCV isolates represented by their cDNA sequences, for example represented by their cDNA sequences in FIG. 2, with said negative numbering of position starting at the nucleotide preceding the first ATG codon of the open reading frame encoding the HCV polyprotein, or with said probe being complementary to the above-defined probes,
detecting the complexes possibly formed between said probe and the nucleotide sequence of the HCV isolate to be identified, and, inferring the type(s) of HCV isolates present from the hybridization pattern.
The above mentioned method can be considered as a method for classifying said isolate according to the percentage of homology with other HCV isolates, according to the fact that isolates belonging to the same type:
exhibit homology of more than 74% at the nucleic acid level in the complete genome,
or exhibit homology of more than 74% at the nucleic acid level in the NS5 region between nucleotide positions 7935 and 8274,
or of which the complete polyprotein shows more than 78% homology at the amino acid level,
or of which the NS5 region between amino acids at positions 2646 and 2758 shows more than 80% homology at the amino acid level,
and according to the fact that HCV isolates belonging to the same subtype exhibit homology of more than 90% at the nucleic acid level in the complete genome and of more than 90% at the amino acid level in the complete polyprotein.
More preferably, said method relates to the classification of HCV isolates according to the fact that,
(1) based on phylogenetic analysis of nucleic acid sequences in the NS5b region between nucleotides 7935 and 8274 (Choo et al., 1991) or 8261 and 8600 (Kato et al., 1990) or 8342 and 8681 (Okamoto et al, 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.34, usually less than 0.33, and more usually of less than 0.32, and isolates belonging to the same subtype show nucleotide distances of less than 0.135, usually of less than 0.13, and more usually of less than 0.125, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.135 to 0.34, usually ranging from 0.14 to 0.33, and more usually ranging from 0.15 to 0.32, and isolates belonging to different HCV types show nucleotide distances greater than 0.34, usually greater than 0.35, and more usually of greater than 0.36,
(2) based on phylogenetic analysis of nucleic acid sequences in the core/E1 region between nucleotides 378 and 957, isolates belonging to the same HCV type show nucleotide distances of less than 0.38, usually of less than 0.37, and more usually of less than 0.36, and isolates belonging to the same subtype show nucleotide distances of less than 0.17, usually of less than 0.16, and more usually of less than 0.15, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.15 to 0.38, usually ranging from 0.16 to 0.37, and more usually ranging from 0.17 to 0.36, and isolates belonging to different HCV types show nucleotide distances greater than 0.36, usually more than 0.365, and more usually of greater than 0.37,
(3) based on phylogenetic analysis of nucleic acid sequences in the NS3/NS4 region between nucleotides 4664 and 5292 (Choo et al., 1991) or between nucleotides 4993 and 5621 (Kato et al., 1990) or between nucleotides 5017 and 5645 (Okamoto et al., 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.35, usually of less than 0.34, and more usually of less than 0.33, and isolates belonging to the same subtype show nucleotide distances of less than 0.19, usually of less than 0.18, and more usually of less than 0.17, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.17 to 0.35, usually ranging from 0.18 to 0.34, and more usually ranging from 0.19 to 0.33, and isolates belonging to different HCV types show nucleotide distances greater than 0.33, usually greater than 0.34, and more usually of greater than 0.35.
The term xe2x80x9canalyte strandxe2x80x9d corresponds to a single- or double-stranded nucleic acid molecule which is suspected to contain sequences which may be present in a biological sample, with said analyte strand being directly detected or detected after amplification. This analyte strand is preferentially positive- or negative-stranded RNA, cDNA, or amplified cDNA.
The expression xe2x80x9cbiological samplexe2x80x9d may refer to any biological sample (tissue or fluid) containing HCV sequences and refers more particularly to blood serum or plasma samples.
The detection of hybrids formed between the type- or subtype-specific target region, if present, and the probes as mentioned above depends on the nature of the reporter molecule used (either present on the probe or on the analyte strand to be targeted) and may be determined by means of calorimetric, fluorescent, radiometric detection or any other method comprised in the state of the art.
The term xe2x80x9c(HCV) isolatesxe2x80x9d refers to any biological fluid containing hepatitis C virus genetic material obtained from naturally infected humans or experimentally infected animals, and also refers to fluids containing hepatitis C virus genetic material which has been obtained from in vitro experiments. For instance, from in vitro cultivation experiments, both cells and growth medium can be employed as a source of HCV genomes material.
The expression xe2x80x9chybridizexe2x80x9d or xe2x80x9ctargetxe2x80x9d refers to a hybridization experiment carried out according to any method known in the art, and allowing the detection of homologous targets (including one or few mismatches) or preferably completely homologous targets (no mismatches allowed).
In the present invention, a sensitive PCR protocol has been used for the highly conserved 5xe2x80x2 UR with sets of nested, universal primers. Positions and sequences of these primers were derived from the sequences of previously reported type 1 and 2 sequences, and the type 3 sequence BR56 (FIG. 2). The obtained amplification product was hybridized to oligonucleotides directed against the variable regions of the 5xe2x80x2 UR, immobilized as parallel lines on membrane strips (reverse-hybridization principle). This hybridization assay, called line probe assay (LiPA), is a rapid assay, by means of which previously poorly described isolates similar to Z4, Z6, and Z7 (Bukh et al., 1992) were detected. A new type 4 classification is proposed for these strains of HCV. Other isolates similar to BE95 and BE96, and to SA1 (Cha et al., 1992) can be distinguished and it is proposed to classify such isolates as type 5a. Isolates similar to HK2 (Bukh et al., 1992) can be distinguished and a new type 6a classification is proposed. A new genotype was detected in isolate BE98, and it is proposed to classify this isolate into HCV type 3, subtype 3c. Another new sequence was detected in GB438, which could be classified as 4f. This LiPA technology allows an easy and fast determination of HCV types and their subtypes present in patient serum.
According to a preferred embodiment of the invention, a set of probes comprising at least two probes is used.
According to a preferred embodiment, in the process of the invention the probe used targets a region of at least 5 nucleotides in one of the following domains:
a) the one extending from nucleotide at position xe2x88x92293 to nucleotide at position xe2x88x92278 in FIG. 2,
b) the one extending from nucleotide at position xe2x88x92275 to nucleotide at position xe2x88x92260 in FIG. 2,
c) the one extending from nucleotide at position xe2x88x92253 to nucleotide at position xe2x88x92238 in FIG. 2,
d) the one extending from nucleotide at position xe2x88x92244 to nucleotide at position xe2x88x92229 in FIG. 2,
e) the on extending from nucleotide at position xe2x88x92238 to nucleotide at position xe2x88x92223 in FIG. 2,
f) the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2,
g) the one extending from nucleotide at position xe2x88x92141 to nucleotide at position xe2x88x92117 in FIG. 2,
h) the one extending from nucleotide at position xe2x88x9283 to nucleotide at position xe2x88x9268 in FIG. 2,
i) the one extending from nucleotide at position xe2x88x92103 to nucleotide at position xe2x88x9288 in FIG. 2,
j) the one extending from nucleotide at position xe2x88x92146 to nucleotide at position xe2x88x92130.
Regions xe2x88x92170 to xe2x88x92155 and xe2x88x92141 to xe2x88x92117 represent variable regions in the linear sequence which may be part of the same stem in the viral RNA. Consequently mutations in one region may be complemented by another mutation in another region to allow or disallow RNA duplex formation. Variation is expected to occur at the same positions in other new types of HCV as well and, therefore, these variable regions might remain instrumental for the discrimination between all current and yet-to-be discovered types of HCV.
According to yet another embodiment the present invention relates to a probe comprising a sequence such that it targets at least one of the following sequences:
AAT TGC CAG GAC GAC C (SEQ ID NO 5)
TCT CCA GGC ATT GAG C (SEQ ID NO 6)
CCG CGA GAC TGC TAG C (SEQ ID NO 7)
TAG CGT TGG GTT GCG A (SEQ ID NO 8)
TTR CCG GRA AGA CTG G (SEQ ID NO 9)
TGR CCG GGC ATA GAG T (SEQ ID NO 10)
TTA CCG GGA AGA CTG G (SEQ ID NO 11)
TGA CCG GAC ATA GAG T (SEQ ID NO 12)
AAT CGC TGG GGT GAC C (SEQ ID NO 13)
TTT CTG GGT ATT GAG C (SEQ ID NO 14)
TCT TGG AGC AAC CCG C (SEQ ID NO 15)
TCT TGG AAC AAC CCG C (SEQ ID NO 16)
AAT YGC CGG GAT GAC C (SEQ ID NO 17)
TTC TTG GAA CTA ACC C (SEQ ID NO 18)
TTT CCG GGC ATT GAG C (SEQ ID NO 19)
TTG GGC GYG CCC CCG C (SEQ ID NO 20)
CCG CGA GAT CAC TAG C (SEQ ID NO 21)
CCG GGA AGA CTG GGT C (SEQ ID NO 22)
CCG GAA AGA CTG GGT C (SEQ ID NO 23)
ACC CAC TCT ATG CCC G (SEQ ID NO 24)
ACC CAC TCT ATG TCC G (SEQ ID NO 25)
ATA GAG TGG GTT TAT C (SEQ ID NO 26)
TCT GCG GAA CCG GTG A (SEQ ID NO 27)
AAT TGC CAG GAY GAC C (SEQ ID NO 28)
GCT CAG TGC CTG GAG A (SEQ ID NO 29)
CCG CGA GAC YGC TAG C (SEQ ID NO 30)
CCC CGC AAG ACT GCT A (SEQ ID NO 31)
CGT ACA GCC TCC AGG C (SEQ ID NO 32)
GGA CCC AGT CTT CCT G (SEQ ID NO 33)
TGC CTG GTC ATT TGG G (SEQ ID NO 34)
TKT CTG GGT ATT GAG C (SEQ ID NO 35)
CCG CAA GAT CAC TAG C (SEQ ID NO 36)
GAG TGT TGT ACA GCC T (SEQ ID NO 37)
AAT CGC CGG GAT GAC C (SEQ ID NO 38)
GAG TGT TGT GCA GCC T (SEQ ID NO 39)
AAT CGC CGG GAC GAC C (SEQ ID NO 40)
AAT GCC CGG CAA TTT G (SEQ ID NO 41)
AAT CGC CGA GAT GAC C (SEQ ID NO 42)
AAT GCT CGG AAA TTT G (SEQ ID NO 43)
GAG TGT CGA ACA GCC T (SEQ ID NO 44)
AAT TGC CGG GAT GAC C (SEQ ID NO 45)
TCT CCG GGC ATT GAG C (SEQ ID NO 46)
AAT TGC CGG GAC GAC C (SEQ ID NO 47)
GGG TCC TTT CCA TTG G (SEQ ID NO 48)
AAT CGC CAG GAT GAC C (SEQ ID NO 49)
TGC CTG GAA ATT TGG G (SEQ ID NO 50)
GAG TGT CGT ACA GCC T (SEQ ID NO 51)
AGT YCA CCG GAA TCG C (SEQ ID NO 52)
GGA ATC GCC AGG ACG A (SEQ ID NO 53)
GAA TCG CCG GGT TGA C (SEQ ID NO 54)
GAG TGT TGT ACA GCC TCC (SEQ ID NO 93)
TGC CCG GAA ATT TGG GC (SEQ ID NO 94)
TGC CCG GAG ATT TGG G (SEQ ID NO 95)
GAG TGT CGA ACA GCC TC (SEQ ID NO 96)
wherein Y represents T or C
K represents G or T
and R represents G or A
or the corresponding sequence wherein T has been replaced by U,
or the sequences which are complementary to the above-defined sequences.
According to another advantagous embodiment of the invention, at least two of the above-mentioned probes or a mixture of two of these probes is used to discriminate between various HCV types or subtypes as defined below.
According to a preferred embodiment of the process of the invention, for each type or subtype of HCV to be determined, a set of two different probes or a mixture of two different probes is used, with each probe of the set or of the mixture respectively targeting a different region chosen among the regions as defined above, and more particularly wherein the two probes, in said set or in said mixture, consist of 10 to 40 contiguous nucleotides respectively targeting two regions respectively chosen from among the following pairs of domains:
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x92141 to nucleotide at position xe2x88x92117 in FIG. 2,
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x92103 to nucleotide at position xe2x88x9288 in FIG. 2,
the one extending from nucleotide at position xe2x88x92141 to nucleotide at position xe2x88x92117 in FIG. 2 and the one extending from nucleotide at position xe2x88x92103 to nucleotide at position xe2x88x9288 in FIG. 2,
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x9283 to nucleotide at position xe2x88x9268 in FIG. 2,
the one extending from nucleotide at position xe2x88x92141 to nucleotide at position xe2x88x92117 in FIG. 2 and the one extending from nucleotide at position xe2x88x9283 to nucleotide at position xe2x88x9268 in FIG. 2,
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x92146 to nucleotide at position xe2x88x92130 in FIG. 2,
the one extending from nucleotide at position xe2x88x92132 to nucleotide at position xe2x88x92117 in FIG. 2 and the one extending from nucleotide at position xe2x88x92146 to nucleotide at position xe2x88x92130 in FIG. 2,
the one extending from nucleotide at position xe2x88x92146 to nucleotide at position xe2x88x92130 in FIG. 2 and the one extending from nucleotide at position xe2x88x92103 to nucleotide at position xe2x88x9288 in FIG. 2.
The invention also relates to a probe having a sequence such that it targets:
the following sequence: TTC TTG GAA CTA ACC C,
or the corresponding sequence wherein T has been replaced by U,
or the sequences which are complementary to the above-defined sequences.
The invention also relates to a set of two probes or mixtures of two probes wherein each of the two probes consists of 10 to 40 contiguous nucleotides, and wherein the two probes respectively target two regions respectively chosen from among the following pairs of domains:
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x92141 to nucleotide at position xe2x88x92117 in FIG. 2,
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x92103 to nucleotide at position xe2x88x9288 in FIG. 2,
the one extending from nucleotide at position xe2x88x92141 to nucleotide at position xe2x88x92117 in FIG. 2 and the one extending from nucleotide at position xe2x88x92103 to nucleotide at position xe2x88x9288 in FIG. 2,
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x9283 to nucleotide at position xe2x88x9268 in FIG. 2,
the one extending from nucleotide at position xe2x88x92141 to nucleotide at position xe2x88x92117 in FIG. 2 and the one extending from nucleotide at position xe2x88x9283 to nucleotide at position xe2x88x9268 in FIG. 2,
the one extending from nucleotide at position xe2x88x92170 to nucleotide at position xe2x88x92155 in FIG. 2 and the one extending from nucleotide at position xe2x88x92146 to nucleotide at position xe2x88x92130 in FIG. 2,
the one extending from nucleotide at position xe2x88x92132 to nucleotide at position xe2x88x92117 in FIG. 2 and the one extending from nucleotide at position xe2x88x92146 to nucleotide at position xe2x88x92130 in FIG. 2,
the one extending from nucleotide at position xe2x88x92146 to nucleotide at position xe2x88x92130 in FIG. 2 and the one extending from nucleotide at position xe2x88x92103 to nucleotide at position xe2x88x9288 in FIG. 2.
According to a preferred embodiment, the invention relates to a process for typing HCV isolates as belonging to at least one of the following HCV types: HCV type 1, HCV type 2, HCV type 3, HCV type 4, HCV type 5, HCV type 6 from a biological sample liable to contain it, and comprises the steps of:
contacting said sample in which the ribonucleotides or deoxyribonucleotides have been made accessible, if need be under suitable denaturation, with at least one probe being capable of hybridizing to a region in the domain extending from nucleotide at position xe2x88x92291 to nucleotide at position xe2x88x9266 of the 5xe2x80x2 UR of HCV isolates represented by their cDNA sequences in FIGS. 2 and 4, with said negative numbering of the nucleotide position starting at the nucleotide preceding the first ATG codon in the open reading frame encoding the HCV polyprotein or with said probe being complementary to the above-defined probes;
detecting the complexes possibly formed between said probe and the target region,and,
inferring the HCV types present from the observed hybridization pattern.
According to a preferred embodiment, the invention relates to a process for typing HCV isolates as belonging to at least one of the following HCV types: HCV type 1, HCV type 2, HCV type 3, HCV type 4, HCV type 5, and HCV type 6, and is such that the probes used are able to target one of the following target regions or said regions wherein T has been replaced by U, or the regions which are complementary to the above-said regions:
for HCV type 1 and 6: AAT TGC CAG GAC GAC C (No. 5)
TCT CCA GGC ATT GAG C (No. 6)
AAT TGC CAG GAY GAC C (No. 28)
for HCV type 1: GCT CAG TGC CTG GAG A (No. 29)
for HCV type 2: TAG CGT TGG GTT GCG A (No. 8)
TTR CCG GRA AGA CTG G (No. 9)
TGR CCG GGC ATA GAG T (No. 10)
TTA CCG GGA AGA CTG G (No. 11)
TGA CCG GAC ATA GAG T (No. 12)
CGT ACA GCC TCC AGG C (No. 32)
CCG GGA AGA CTG GGT C (No. 22)
CCG GAA AGA CTG GGT C (No. 23)
ACC CAC TCT ATG CCC G (No. 24)
ACC CAC TCT ATG TCC G (No. 25)
ATA GAG TGG GTT TAT C (No. 26)
GGA CCC AGT CTT CCT G (No. 33)
TGC CTG GTC ATT TGG G (No. 34)
for HCV type 3: AAT CGC TGG GGT GAC C (No. 13)
TTT CTG GGT ATT GAG C (No. 14)
CCG CGA GAT CAC TAG C (No. 21)
CCG CAA GAT CAC TAG C (No. 36)
GAA TCG CCG GGT TGA C (No. 54)
for HCV type 4 and 5: AAT YGC CGG GAT GAC C (No. 17)
for HCV type 4: TTC TTG GAA CTA ACC C (No. 18)
for HCV type 4, 3c and 3b: TTT CCG GGC ATT GAG C (No. 19)
for HCV type 4 and 3b: AAT CGC CGG GAT GAC C (No. 38)
for HCV type 4: GAG TGT TGT ACA GCC T (No. 37)
GAG TGT TGT GCA GCC T (No. 39)
AAT CGC CGG GAC GAC C (No. 40)
AAT GCC CGG CAA TTT G (No. 41)
AAT CGC CGA GAT GAC C (No. 42)
AAT GCT CGG AAA TTT G (No. 43)
AAT CGC CAG GAT GAC C (No. 49)
TGC CTG GAA ATT TGG G (No. 50)
GGA ATC GCC AGG ACG A (No. 53)
for HCV type 5: AAT TGC CGG GAT GAC C (No. 45)
AAT TGC CGG GAC GAC C (No. 47)
TCT CCG GGC ATT GAG C (No. 46)
GAG TGT CGA ACA GCC T (No. 44)
for HCV type 6: GGG TCC TTT CCA TTG G (No. 48)
wherein Y represents C or T, and K represents G or T, or the probes used are a set of two probes chosen from among the above-defined probes.
The invention also relates to the use of the above-defined method for determining the type(s) of HCV isolates present in a biological sample.
The term xe2x80x9ctypexe2x80x9d corresponds to a group of HCV isolates of which the complete genome shows more than 74% homology at the nucleic acid level, or of which the NS5 region between nucleotide positions 7935 and 8274 shows more than 74% homology at the nucleic acid level, or of which the complete HCV polyprotein shows more than 78% homology at the amino acid level, or of which the NS5 region between amino acids at positions 2646 and 2758 shows more than 80% homology at the amino acid level, to genomes of the other isolates of the group, with said numbering beginning with the first ATG codon or methionine of the HCV polyprotein of the HCV-J isolate (Kato et al., 1990). Isolates belonging to different types of HCV exhibit homologies of less than 74% at the nucleic acid level and less than 78% at the amino acid level. Isolates belonging to the same type usually show homologies of about 92 to 95% at the nucleic acid level and 95 to 96% at the amino acid level when belonging to the same subtype, and those belonging to the same type but different subtypes preferably show homologies of about 79% at the nucleic acid level and 85-86% at the amino acid level. More preferably, classification of HCV isolates should be performed according to the fact that,
(1) based on phylogenetic analysis of nucleic acid sequences in the NS5b region between nucleotides 7935 and 8274 (Choo et al., 1991) or 8261 and 8600 (Kato et al., 1990) or 8342 and 8681 (Okamoto et al, 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.34, usually less than 0.33, and more usually of less than 0.32, and isolates belonging to the same subtype show nucleotide distances of less than 0.135, usually of less than 0.13, and more usually of less than 0.125, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.135 to 0.34, usually ranging from 0.14 to 0.33, and more usually ranging from 0.15 to 0.32, and isolates belonging to different HCV types show nucleotide distances greater than 0.34, usually greater than 0.35, and more usually of greater than 0.36,
(2) based on phylogenetic analysis of nucleic acid sequences in the core/E1 region between nucleotides 378 and 957, isolates belonging to the same HCV type show nucleotide distances of less than 0.38, usually of less than 0.37, and more usually of less than 0.36, and isolates belonging to the same subtype show nucleotide distances of less than 0.17, usually of less than 0.16, and more usually of less than 0.15, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.15 to 0.38, usually ranging from 0.16 to 0.37, and more usually ranging from 0.17 to 0.36, and isolates belonging to different HCV types show nucleotide distances greater than 0.36, usually more than 0.365, and more usually of greater than 0.37,
(3) based on phylogenetic analysis of nucleic acid sequences in the NS3/NS4 region between nucleotides 4664 and 5292 (Choo et al., 1991) or between nucleotides 4993 and 5621 (Kato et al., 1990) or between nucleotides 5017 and 5645 (Okamoto et al., 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.35, usually of less than 0.34, and more usually of less than 0.33, and isolates belonging to the same subtype show nucleotide distances of less than 0.19, usually of less than 0.18, and more usually of less than 0.17, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.17 to 0.35, usually ranging from 0.18 to 0.34, and more usually ranging from 0.19 to 0.33, and isolates belonging to different HCV types show nucleotide distances greater than 0.33, usually greater than 0.34, and more usually of greater than 0.35.
According to a preferred embodiment of this invention any of the probes designated with SEQ ID NO 5, 28 and 6 may be used to identify the type 1; any of the probes with SEQ ID NO 8 to 12 or 22 to 26 and 32 to 34 may be used to identify type 2; and any of the probes with SEQ ID NO 13, 14, 36, 21, or 54 to identify type 3; and any of the probes with SEQ ID NO 17, 18 or 19 and 37 to 43 and probes of SEQ ID NO 49, 50 and 53 to identify type 4.
Probes 44 to 47 may be used to identify type 5, probe 48 may be used to identify type 6.
The following regions might also be used for discrimination of certain types: the region between positions xe2x88x92238 to xe2x88x92223 for type 2, the region between positions xe2x88x92244 to xe2x88x92229 for type 4, the regions between positions xe2x88x92253 to xe2x88x92238, or between positions xe2x88x92275 to xe2x88x92260, or between positions xe2x88x92293 to xe2x88x92278 for type 3.
The nucleotide at position xe2x88x922 can also be employed to further discriminate between certain types or subtypes.
The process of the invention also comprises the discrimination and classification of subtypes of HCV, wherein besides the above-mentioned probes also probes hybridizing to the following target regions are used, or said regions wherein T is replaced by U or said regions which are complementary to the above-defined regions,
for HCV type 1, subtype 1a:
CCC CGC AAG ACT GCT A (No. 31)
for HCV type 1, subtype 1b:
CCG CGA GAC TGC TAG C (No. 7)
CCG CGA GAC YGC TAG C (No. 30)
wherein Y represents C or T,
for HCV type 2, subtype 2a:
TTR CCG GRA AGA CTG G (No. 9)
TGR CCG GGC ATA GAG T (No. 10)
CCG GGA AGA CTG GGT C (No. 22)
ACC CAC TCT ATG CCC G (No. 24)
wherein R represents A or G,
for HCV type 2, subtype 2b:
TTA CCG GGA AGA CTG G (No. 11)
TGA CCG GAC ATA GAG T (No. 12)
CCG GAA AGA CTG GGT C (No. 23)
ACC CAC TCT ATG TCC G (No. 25)
for HCV type 2, subtype 2c:
GGA CCC AGT CTT CCT G (No. 33)
TGC CTG GTC ATT TGG G (No. 34)
for HCV type 3, subtype 3a:
AAT CGC TGG GGT GAC C (No. 13)
TTT CTG GGT ATT GAG C (No. 14)
TKT CTG GGT ATT GAG C (No. 35)
wherein K represents G or T,
for HCV type 3, subtype 3b:
TTT CCG GGC ATT GAG C (No. 19)
AAT CGC CGG GAT GAC C (No. 38)
CCG CGA GAT CAC TAG C (No. 21)
for HCV type 3, subtype 3c:
GAG TGT CGT ACA GCC T (No. 51)
GAA TCG CCG GGT TGA C (No. 54)
TTT CCG GGC ATT GAG C (No. 19)
CCG CGA GAC TGC TAG C (No. 7)
for HCV type 4, subtype 4a or 4d:
AAT CGC CGG GAT GAC C (No. 38)
TTT CCG GGC ATT GAG C (No. 19)
for type 4, subtype 4b:
AAT CGC CGG GAT GAC C (No. 38)
AAT GCC CGG CAA TTT G (No. 41)
AAT CGC CGG GAC GAC C (No. 40)
for type 4, subtype 4c:
AAT CGC CGA GAT GAC C (No. 42)
AAT GCT CGG AAA TTT G (No. 43)
TGC CTG GAA ATT TGG G (No. 50)
GGA ATC GCC AGG ACG A (No. 53)
CCG CGA GAC TGC TAG C (No. 7)
for type 4, subtype 4e:
AAT CGC CGG GAC GAC C (No. 40)
GAG TGT TGT GCA GCC T (No. 39)
AAT GCC CGG CAA TTT G (No. 41)
for type 4, subtype 4f:
TTT CCG GGC ATT AGC C (No. 19)
AAT CGC CGG GAT GAC C (No. 38)
GAG TGT CGT ACA GCC T (No. 51)
CCG CGA GAC TGC TAG C (No. 7)
for type 4, subtype 4g (provisional):
TGC CTG GAA ATT TGG G (No. 50)
GGA ATC GCC AGG ACG A (No. 53)
for type 4, subtype 4h (provisional):
AAT CGC CAG GAT GAC C (No. 49)
TGC CTG GAA ATT TGG G (No. 50)
or the probes used are a set of two probes chosen from among the defined probes.
The invention also relates to the use of the above-defined method for determining the HCV subtype(s) present in a biological sample to be analyzed.
The term xe2x80x9csubtypexe2x80x9d corresponds to a group of HCV isolates of which the complete genome or complete polyprotein shows a homology of more than 90% both at the nucleic acid and amino acid levels, or of which the region in NS5 between nucleotide positions 7935 and 8274 shows a homology of more than 88% at the nucleic acid level to the corresponding parts of the genomes of the other isolates of the same group, with said numbering beginning with the adenine residue of the initiation coding of the long ORF. Isolates belonging to different subtypes of HCV and belonging to the same type of HCV show homologies of more than 74% at the nucleic acid level and of more than 78% at the amino acid level.
More preferably the above mentioned process relates to classification of HCV isolates into type and subtypes should be performed according to the fact that,
(1) based on phylogenetic analysis of nucleic acid sequences in the NS5b region between nucleotides 7935 and 8274 (Choo et al., 1991) or 8261 and 8600 (Kato et al., 1990) or 8342 and 8681 (Okamoto et al, 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.34, usually less than 0.33, and more usually of less than 0.32, and isolates belonging to the same subtype show nucleotide distances of less than 0.135, usually of less than 0.13, and more usually of less than 0.125, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.135 to 0.34, usually ranging from 0.14 to 0.33, and more usually ranging from 0.15 to 0.32, and isolates belonging to different HCV types show nucleotide distances greater than 0.34, usually greater than 0.35, and more usually of greater than 0.36,
(2) based on phylogenetic analysis of nucleic acid sequences in the core/E1 region between nucleotides 378 and 957, isolates belonging to the same HCV type show nucleotide distances of less than 0.38, usually of less than 0.37, and more usually of less than 0.36, and isolates belonging to the same subtype show nucleotide distances of less than 0.17, usually of less than 0.16, and more usually of less than 0.15, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.15 to 0.38, usually ranging from 0.16 to 0.37, and more usually ranging from 0.17 to 0.36, and isolates belonging to different HCV types show nucleotide distances greater than 0.36, usually more than 0.365, and more usually of greater than 0.37,
(3) based on phylogenetic analysis of nucleic acid sequences in the NS3/NS4 region between nucleotides 4664 and 5292 (Choo et al., 1991) or between nucleotides 4993 and 5621 (Kato et al., 1990) or between nucleotides 5017 and 5645 (Okamoto et al., 1991), isolates belonging to the same HCV type show nucleotide distances of less than 0.35, usually of less than 0.34, and more usually of less than 0.33, and isolates belonging to the same subtype show nucleotide distances of less than 0.19, usually of less than 0.18, and more usually of less than 0.17, and consequently isolates belonging to the same type but different subtypes show nucleotide distances ranging from 0.17 to 0.35, usually ranging from 0.18 to 0.34, and more usually ranging from 0.19 to 0.33, and isolates belonging to different HCV types show nucleotide distances greater than 0.33, usually greater than 0.34, and more usually of greater than 0.35,
Using these criteria, HCV isolates can be classified into at least 6 types.
Several subtypes can clearly be distinguished in types 1, 2, 3 and 4 (1a, 1b, 2a, 2b, 2c, 3a, 3b, 3c, 4a, 4b, 4c, 4d, 4e and 4f) based on homologies of the 5xe2x80x2 UR and coding regions including the part of NS5 between positions 7935 and 8274 and the C/E1 region between nucleotides 317 and 957, and based on comparisons with isolates Z1 and DK13 as described in Bukh et al. (1993).
Further subdivision of type 4 into subtypes 4g and 4h is tentative and only based on differences in the 5xe2x80x2 UR. An overview of most of the reported isolates and their proposed classification according to the typing system of the present invention is given in Table 1.
According to a preferred embodiment of the present invention, the probe with SEQ ID NO 31 may be used to identify subtype 1a; the probes with SEQ ID NO 7 and 30 may be used to identify subtype 1b; any of the probes with SEQ ID NO 9, 10, 22, or 24 may be used to identify subtype 2a; any of the probes with SEQ ID NO 11, 12, 23, or 25 may be used to identify subtype 2b; any of the probes with SEQ ID NO 33 or 34 may be used to identify subtype 2c; any of the probes with SEQ ID NO 13, 14, or 35 may be used to identify subtype 3a; any of the probes with SEQ ID NO 38, 19 and 21 may be used to identify subtype 3b, 4a or 4d; any of the probes with SEQ ID NO 38 or 41 may be used to identify subtype 4b; any of the probes with SEQ ID NO 42 or 43 may be used to identify subtype 4c; any of the probes in SEQ ID NO 39, 40, or 41 may be used to identify: 4e, 51, 38, 19, or 7; 4f; any of the probes with SEQ ID NO 49 or 50 may be used to identify the putative subtype 4h; any of the probes with SEQ ID NO 50 or 53 may be used to identify the putative subtype 4g.
According to a preferred embodiment of the process of the invention, the HCV types or subtypes to be discriminated are also identified by means of universal probes for HCV, such as the ones targeting one of the following regions:
TTG GGC GYG CCC CCG C (No. 20)
TCT GCG GAA CCG GTG A (No. 27)
According to another advantageous embodiment of the process of the invention, the hybridization step is preceeded by an amplification step of the deoxyribonucleotide or ribonucleotide containing the region to target, advantageously comprising the following steps:
contacting the biological sample liable to contain the isolate to be typed or subtyped with a set of primers, flanking the region to target, with said primers being complementary to conserved regions of the HCV genome, and preferably primers being complementary to the 5xe2x80x2 untranslated conserved regions of the HCV genome, with said primers preferably having at least 8 contiguous nucleotides more preferably about 15, and even more preferably more than 15 contiguous nuclotides, with said contiguous nucleotides being respectively complementary to sequences chosen from the region extending from nucleotide xe2x88x92341 to nucleotide xe2x88x92171 and from the region extending from nucleotide xe2x88x9267 to nucleotide xe2x88x921, of FIGS. 2 and 4.
Alternatively, the antisense primers could also extend into the core region or the set of primers may or/be aimed at amplifying both the 5xe2x80x2UR and the core region, either in 1 PCR fragment or with a set of primers for each of the two regions. Consequently, probes from the core region, able to hybrize to (sub)type specific regions in core PCR products, may be included in the line probe assay to further discriminate between types and/or subtypes,
amplifying the target region, for instance via a polymerase chain reaction by means of the above-mentioned set of primers and possibly incorporating a label such as digoxigenin or biotin into the amplified target sequence, with said amplifying being repeated between 20 and 80 times, advantageously between 30 and 50 times.
According to a preferred embodiment of the invention, the analyte strand may be enzymatically or chemically modified either in vivo or in vitro prior to hybridization. Many systems for coupling reporter groups to nucleic acid compounds have been described, based on the use of such labels as biotin or digoxigenin. In still another embodiment of the invention sandwich hybridization may be used. In a preferred embodiment, the target sequence present in the analyte strand is converted into cDNA, with said cDNA being amplified by any technique known in the art such as by the polymerase chain reaction (PCR; Saiki et al., 1988), ligase chain reaction (LCR; Landegren et al., 1988; Wu and Wallace, 1989; Barany, 1991), nucleic acid sequence-based amplification (NASBA; Guatelli et al., 1990; Compton, 1991), transcription-based amplification system (TAS; Kwoh et al., 1989), strand displacement amplification (SDA; Duck, 1990; Walker et al., 1992) or amplification by means of Qb replicase (Lizardi et al., 1988; Lomeli et al., 1989).
The cDNA amplification step is preferably achieved by means of PCR technology and may consist of steps:
(a) providing a set of primers for a polymerase chain reaction method which flank the target sequence to be detected;
(b) amplifying the target region via a polymerase chain reaction method by means of the primers of (a); and in the same step an appropriate label molecule can be incorporated into the amplified target said label molecule being preferably digoxigenin or biotin.
The term xe2x80x9cprimersxe2x80x9d corresponds to oligonucleotide sequences being complementary to conserved regions of sense or antisense strands of cDNA or RNA derived from the HCV genome; preferably of the 5xe2x80x2 untranslated conserved regions of the HCV genome and more preferably selected from conserved regions of the 5xe2x80x2 untranslated region of the HCV genome comprising positions xe2x88x92341 to xe2x88x92171 and xe2x88x9267 to xe2x88x921, or the core region.
In an advantageous embodiment of the invention, the process is such that amplification consists of a double PCR step, each step involving a specific set of primers, with the said first step involving outer primers selected from the region extending from nucleotide xe2x88x92341 to nucleotide xe2x88x92186 and from the region extending from nucleotide xe2x88x9252 to nucleotide xe2x88x921, and more particularly the following set:
CCC TGT GAG GAA CTW CTG TCT TCA CGC (No. 1)
GGT GCA CGG TCT ACG AGA CCT (No. 2)
or their complements,
wherein W represents A or T, and with the second step involving nested primers selected from the region extending from nucleotide xe2x88x92326 to nucleotide xe2x88x92171 and from the region extending from nucleotide xe2x88x9268 to nucleotide xe2x88x921 and, more particularly the following set:
TCT AGC CAT GGC GTT AGT RYG AGT GT (No. 3)
CAC TCG CAA GCA CCC TAT CAG GCA GT (No. 4)
wherein R represents A or G and Y represents T or C
or their complements.
According to this embodiment of the invention, a double PCR is performed with outer primers in the first round including sequences as shown in SEQ ID NO 1 and 2, or their complementary sequences and with nested primers for the second round including sequences as shown in SEQ ID NO 3 and 4, or their complementary sequences.
The term xe2x80x9cappropriate label moleculexe2x80x9d may include the use of labeled nucleotides incorporated during the polymerase step of the amplification such as illustrated in Saiki et al. (1988) and Bej et al. (1990) and or any other method known to the person skilled in the art.
The assays as described in this invention may be improved in several ways obvious for the person skilled in the art. For example the cPCR reactions can be preceded by an RNA-capture step.
According to yet another embodiment, the present invention relates to a composition comprising at least one oligonucleotide primer, with said primers preferably having at least 15 contiguous nucleotides, with said contiguous nucleotides being respectively complementary to sequences chosen from the region extending from nucleotide xe2x88x92341 to nucleotide xe2x88x92171 and from the region extending from nucleotide xe2x88x9267 to nucleotide xe2x88x921(, of FIG. 2), or their complement.
According to yet another embodiment, the present invention relates to a composition comprising at least one oligonucleotide primer preferably having at least 15 contiguous nucleotides, with said contiguous nucleotides being chosen from any of the following sequences:
CCC TGT GAG GAA CTW CTG TCT TCA CGC (No. 1)
GGT GCA CGG TCT ACG AGA CCT (No. 2)
TCT AGC CAT GGC GTT AGT RYG ACT GT (No. 3)
CAC TCG CAA GCA CCC TAT CAG GCA GT (No. 4)
wherein W represents A or T, R represents A or G, and Y represents T or C,
or their complements.
According to an advantageous embodiment, the process of the invention for the simultaneous typing of all HCV isolates contained in a biological sample comprises the step of contacting one of the following elements:
either said biological sample in which the genetic material is made available for hybridization,
or the purified genetic material contained in said biological sample,
or single copies derived from the purified genetic material,
or amplifified copies derived from the purified genetic material,
with a solid support on which probes as defined above, have been previously immobilized.
According to this preferred embodiment of the invention, the probes as defined above are immobilized to a solid susbstrate.
The term xe2x80x9csolid substratexe2x80x9d can refer to any substrate to which an oligonucleotide probe can be coupled, provided that it retains its hybridization characteristics and provided that the background level of hybridization remains low. Usually the solid substrate will be a microtiter plate or a membrane (e.g. nylon or nitrocellulose).
Prior to application to the membrane or fixation it may be convenient to modify the nucleic acid probe in order to facilitate fixation or improve the hybridization efficiency. Such modifications may encompass homopolymer tailing, coupling with different reactive groups such as aliphatic groups, NH2 groups, SH groups, carboxylic groups, or coupling with biotin or haptens.
According to an advantageous embodiment of the invention, the process comprises the step of contacting anyone of the probes as defined above, with one of the following elements:
either a biological sample in which the genetic material is made available for hybridization,
or the purified genetic material contained in said biological sample,
or a single copy derived from the purified genetic material,
or an amplified copy derived from the purified genetic material, with said elements being previously immobilized on a support.
The invention also relates to the typing of new isolates.
More particulary the invention relates to a process for the detection and identification of novel HCV types or subtypes different from the known types or subtypes and comprising the steps of:
determining to which known types or subtypes the HCV isolate present in the biological sample belongs to, according to the process as defined above, possibly with said biological sample being previously determined as containing HCV, possibly by means of HCV antigen or antibody assays or with a universal probe for HCV, such as those defined above,
in the case of observing a sample which does not hybridize positively with at least one of the probes able to target the regions chosen from any of the two domains as defined above, sequencing the complete genome of the HCV type present in the sample, or alternatively sequencing that (the) portion(s) of the 5xe2x80x2 untranslated region of the sample corresponding to a new type and/or subtype to be determined.
Advantageously the process for the detection and identification of novel HCV types and/or subtypes, present in a biological sample, which are different from type 1, type 2, type 3, type 4, type 5, type 6, in the case of identifying a novel type; and which are different from subtypes 1a and 1b for a type 1 HCV isolate, from subtypes 2a, 2b, and 2c for a type 2 isolate, from subtypes 3a, 3b and 3c for a type 3 isolate, from subtypes 4a, 4b, 4c, 4d, 4e, 4f, 4g and 4h for a type 4 isolate; from subtype 5a for a type 5 isolate; from subtype 6a for a type 6 isolate, in the case of identifying a novel subtype, and comprising the steps of:
determining to which known type(s) or subtype(s) the HCV isolate(s) present in the biological sample to be analyzed belongs, according to the process of the invention, possibly with said biological sample being previously determined as containing HCV, possibly by means of HCV antigen or antibody assays or with a universal probe for HCV such as the one defined above,
in the case of observing a sample which does not hybridize to at least one of the probes able to target the regions chosen from any of the type specific or subtype specific domains as defined above, more particulary not hybridizing with SEQ ID NO 5, 28 and 6 for type 1, with SEQ ID NO 8 to 12 or 22 to 26 and 32 to 34 for type 2, with SEQ ID NO 13, 14, 36, 21 or 54 for type 3, and with SEQ ID NO 17, 18, 19, 37 to 43, 49, 50 and 53 for type 4; and with SEQ ID NO 7 and 30 for subtype 1b, with SEQ ID NO 31 for subtype 1a, with SEQ ID NO 9, 10, 22 or 24 for subtype 2a, with SEQ ID NO 11, 12, 23 or 25 for subtype 2b, with SEQ ID NO 33 or 34 for subtype 2c, with SEQ ID NO 13, 14 or 35 for subtype 3a, with SEQ ID NO 38, 21 and 19 for subtype 3b, 4a or 4d, with SEQ ID NO 38 or 41 for subtype 4b; with SEQ ID NO 42 or 43 for subtype 4c; with SEQ ID NO 39, 40, or 41 for subtype 4e, with SEQ ID NO 51, 38, 19 or 7; for subtype 4f; with SEQ ID NO 49 or 50 for the putative subtype 4h; with SEQ ID NO 50 or 53 for the putative subtype 4g, sequencing the complete genome of the HCV type present in the sample, or, alternatively sequencing that (the) portion(s) of the 5xe2x80x2 untranslated region of the sample corresponding to a new type and/or subtype to be determined.
The term xe2x80x9cnew isolatesxe2x80x9d corresponds to isolates which are not able to hybridize to any of the 9 above-mentioned regions or show reactivities which cannot be correctly interpreted as matching one of the currently known HCV types or subtypes. This special embodiment of the invention may also be performed by the steps of:
(a) screening HCV antibody-positive sera, or clinical NANB hepatitis samples, or a population of random samples, by cPCR (cDNA PCR),
(b) performing a HCV LiPA with those samples from which a cPCR product has been obtained, and
(c) cloning and sequencing these PCR fragments showing aberrant reactivities.
The invention also relates to a method for determining the type(s) as well as the subtypes(s) of HCV, and/or HIV, and/or HBV and/or HTLV present in a biological sample, which comprises the steps of:
providing:
at least one of the probes as defined above, preferably the probes as defined above, enabling the genotyping (typing and/or subtyping) of HCV, and at least one of the following probes:
probes capable of detecting oligonucleotides of HIV types 1 and/or 2 which can be present in said biological sample, and/or
probes capable of detecting oligonucleotides of HBV subtypes, and /or sAg mutants, and/or cAg mutants which can be present in said biological sample, and/or
probes capable of detecting oligonucleotides of HTLV-I and/or HTLV-II suspected to be in the biological sample,
possibly providing a set of primers as defined above, as well at least one of the following primers: sets of primers to respectively amplify human immunodeficency virus (HIV), and/or HBV and/or human T-cell lymphotropic virus (HTLV) oligonucleotides, by means of PCR reaction and amplifying the oligonucleotides of HCV, and either HBV and/or HIV and/or HTLV possibly present in the biological sample,
contacting
the biological sample in which the genetic material is made available for hybridization,
or the purified genetic material contained in said biological sample,
or single copies derived from the purified genetic material,
or amplified copies derived from the purified genetic material,
with the above-mentioned probes defined above under conditions which allow hybridization between the probes and the target sequences of isolates of HCV and at least one of the following viruses: HBV, and/or HIV, and/or HTLV,
detecting the complexes possibly formed between the probes used and the target regions possibly present in the biological sample.
According to this embodiment, in addition to the type or subtype of HCV present in a biological sample, the invention also relates to a method for determining the type or subtype of any other parenterally transmitted viral isolate such as HTLV, HIV, HBV characterized by incorporating on one and the same strip, probes hybridizing specifically to:
the different types and/or subtypes of HCV as defined above,
human immunodeficiency viruses HIV-1 and HIV-2,
human T-cell lymphotrophic viruses HTLV-1 and HTLV-2,
the different HB surface antigen (HBsAg) mutants or HB core antigen (HBcAg) or HB precore Ag mutants.
In some test samples, different target sequences of which the specific detection is of clinical relevance are present simultaneously. For each of these target sequences a separate hybridization test with the corresponding probe should be performed. The combination of different type/subtype specific probes comprised in the art, in combination with the new and inventive HCV type/subtype-specific probes as explained in the present invention on one membrane strip could provide an easy and reliable general typing system for parenterally transmitted human viral diseases. If analyte strand amplification is necessary, a set of primers can be provided per viral organism to be differentiated and classified.
The invention also relates to a solid support, particularly a membrane strip containing, on known locations of its surface, a selection of the following probes, or their complements, or the above-mentioned probes wherein T has been replaced by U:
NO5, NO6, NO7, NO8, NO9, NO 10, NO 11, NO 12, NO 13, NO 14, NO 15, NO 16, NO 17, NO 18, NO 19, NO 20, NO 21, NO 22, NO 23, NO 24, NO 25, NO 26, NO 27, NO 28 to 54 and NO 93 to 96, as defined above, as well as a control to determine if there is hybridization between these probes and the ribo or deoxyribonucleotide strands of HCV, liable to be contained in a biological sample in which HCV isolates are to be differentiated.
According to a specially preferred embodiment of the invention, the probes are immobilized in a line-wise fashion to a membrane strip.
In this preferred embodiment of the invention, a set of probes each applied to a known location onto the membrane strip include probes selected from the sequences with SEQ ID NO 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, SEQ ID NO 28 to 54, and NO 93 to 96 as well as a control line for conjugate binding.
The method of this preferred embodiment of the invention makes it possible to quickly determine the type of HCV infection. This assay provides the ability to discriminate between at least 6 different HCV types and might discriminate between at least 18 subtypes, and is a good instrument for searching for new types or (sub)types of HCV. For example, new subtypes 1c, 1d and type 7, and other new (sub)types may contain specific mutations in the regions mentioned above, which can be employed for specific detection by means of type-specific probes derived from such new sequences.
The invention also relates to a kit for the in vitro discrimination of at least one HCV isolate from a biological sample liable to contain it, and for its classification it according to the HCV type and subtype, with said kit containing
a least one probe selected among any of those defined above;
a buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the cDNAs and/or RNAs of HCV isolates to be carried out;
when appropriate, means for detecting the hybrids resulting from the preceding hybridization.
The invention also relates to a kit for typing at least one HCV isolate from a biological sample liable to contain it and for classifying it according to the HCV type and subtype, with said kit containing
possibly one universal probe as defined above,
at least one probe selected among any of those of the invention,
a buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the DNAs and/or RNAs of HCV isolates to be carried out;
when appropriate, means for detecting the hybrids resulting from the preceding hybridization.
According to this embodiment, the invention also relates to a kit for genotyping (typing and/or subtyping) of HCV isolates comprising:
a set of probes as defined above, preferentially immobilized on a solid substrate, and more preferentially on one and the same membrane, and
possibly a set of primers as defined above,
a set of buffers necessary to carry out the hybridization as well as the detection of the hybrids formed.
The invention also relates to a kit for typing HCV isolates belonging to at least one of the following HCV types: HCV type 1, HCV type 2, HCV type 3, HCV type 4, HCV type 5, HCV type 6 with said kit containing at least one of the probes as above defined,
the buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the cDNAs and/or RNAs of the above-mentioned HCV isolates to be carried out;
when appropriate, means for detecting the hybrids resulting from the preceding hybridization.
The invention advantageously relates to a kit for the discrimination and classification of HCV types and subtypes, with said kit containing:
at least one of the probes as defined above,
the buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the DNAs and/or RNAs of the above-mentioned HCV isolates to be carried out;
when appropriate, means for detecting the hybrids resulting from the preceding hybridization.
It is to be mentioned that all the probes from SEQ ID NO 1 to SEQ ID NO 54 and SEQ ID NO 93 to 96 are new.
Furthermore, probes of SEQ ID NO 18, 29, 33, 34, 35, 40, 42, 43, 47, 49 and 54 are derived from new sequences.